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Alchemical free energy calculations employ unphysical ("alchemical") intermediates to estimate the free energies of various physical processes. Such process include ligand binding to a protein receptor, the transfer of a small molecule from gas to water, or the free energy of a mutation of a side chain. This approach provides not only a quantitative and rigorous method for computing free energies, but often provides insight into the dominant interactions driving binding. With over 700 articles. And p...

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AlchemistryWiki | alchemistry.org Reviews

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Alchemical free energy calculations employ unphysical (alchemical) intermediates to estimate the free energies of various physical processes. Such process include ligand binding to a protein receptor, the transfer of a small molecule from gas to water, or the free energy of a mutation of a side chain. This approach provides not only a quantitative and rigorous method for computing free energies, but often provides insight into the dominant interactions driving binding. With over 700 articles. And p...

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AlchemistryWiki | alchemistry.org Reviews

https://alchemistry.org

Alchemical free energy calculations employ unphysical ("alchemical") intermediates to estimate the free energies of various physical processes. Such process include ligand binding to a protein receptor, the transfer of a small molecule from gas to water, or the free energy of a mutation of a side chain. This approach provides not only a quantitative and rigorous method for computing free energies, but often provides insight into the dominant interactions driving binding. With over 700 articles. And p...

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alchemistry.org

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About the Editors - AlchemistryWiki

http://www.alchemistry.org/wiki/About_the_Editors

Michael R Shirts - an assistant professor at The University of Virginia. In the department of chemical engineering. He has done a number of studies on free energy methods and calculation: see Michael Shirts' group page. Levi Naden - a graduate student in the Shirts Group. Working on free energy calculation methods. An assistant professor at University of California-Irvine. John D Chodera - an Assistant Member at the Memorial Sloan-Kettering Cancer Center. Free Energy References (external).

2

Events - AlchemistryWiki

http://www.alchemistry.org/wiki/Events

2016 Workshop on Free Energy Methods in Drug Design: Targeting Cancer. 2016 Workshop on Kinetics and Markov State Models in Drug Design. 2014 Workshop on Free Energy Methods in Drug Design. 2012 Workshop on Free Energy Methods in Drug Design. 2010 Workshop on Free Energy Methods in Drug Design. Retrieved from " http:/ www.alchemistry.org/wiki/index.php? Free Energy References (external). This page was last modified on 20 May 2016, at 14:14.

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Proper referencing - AlchemistryWiki

http://www.alchemistry.org/wiki/Proper_referencing

Citing with the Cite. Citing with the Template and CiteULike. Selecting a unique name. Information in the reference. Citing with the Cite. Extension is a handy and intuitive extension that lets you cite with superscripts and create a reference list at the bottom of a page. The official usage page. Has very easy to follow instructions on how to cite correctly in an article, and some of the methods will be recapped here. The extension uses an HTML tag, ref. To create the reference. Note: You will need the ...

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The Simple Molecular Benchmark Test Set - AlchemistryWiki

http://www.alchemistry.org/wiki/Special:Random

The Simple Molecular Benchmark Test Set. Direct editing is disabled; please visit [1]. Simple Molecule Benchmark Test Set (v1.0). Improvements to the Benchmark Test Set. Extensions to other programs. Future simple molecular sets problems to tackle. Simple Molecule Benchmark Test Set (v1.0). Problem 1) Is the method at all valid for molecular systems? System: Simplest molecular free energy system = UA methane in TIP3P water. Problem 2) Can the method handle water rearrangement around charges? In each case...

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Recent changes - AlchemistryWiki

http://www.alchemistry.org/wiki/Special:RecentChanges

Track the most recent changes to the wiki on this page. This edit created a new page (also see list of new pages. This is a minor edit. This edit was performed by a bot. The page size changed by this number of bytes. Changes in last 1. Show new changes starting from 08:20, 19 August 2016. 160; 11:40 . Constructing a Pathway of Intermediate States. 160; . 160; . 160; 11:17 . User account Samar jhu. Retrieved from " http:/ www.alchemistry.org/wiki/Special:RecentChanges.

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Chodera lab / MSKCC. Chodera lab / MSKCC. Chodera lab / MSKCC. Changing drug discovery one ratio of partition functions at a time. Chodera lab / MSKCC. See the Chodera lab. We contribute applications and tools to the Omnia suite. Of molecular modeling and simulation tools based on the OpenMM. GPU-accelerated molecular modeling package. An open, extensible platform for GPU-accelerated alchemical binding free energy calculations. Using the OpenMM toolkit.

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Links — Chodera lab // MSKCC

http://www.choderalab.org/links

Chodera lab / MSKCC. Chodera lab / MSKCC. Chodera lab / MSKCC. Changing drug discovery one ratio of partition functions at a time. Chodera lab / MSKCC. Collaborators and useful links. Alchemical free energy calculations. Information resource for alchemical free energy calculations. Michael R. Shirts, Department of Chemical Engineering, University of Virginia. David L. Mobley, Pharmaceutical Sciences, University of California, Irvine. Vijay S. Pande, Department of Chemistry, Stanford University.

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Mobley Lab Resources - Pharmaceutical Sciences - University of California, Irvine

http://www.mobleylab.org/resources.html

Resources: Lab Facilities, Useful Information, Etc. This page is still under construction.). Automatic setup of relative free energy calculations in GROMACS. An open tool implementing some recommended practices for analyzing alchemical free energy calculations. Adjusts topology files with GAFF to have GAFF-DC charges. Tools for Small Molecules, Antechamber, OpenMM, and More. Tools for setting up arbitrary (currently non-water) solute-solvent mixtures for simulation in GROMACS or AMBER formats. Lab facili...

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Mobley Lab - Pharm. Sci. - University of California, Irvine

http://www.mobleylab.org/index.html

David L. Mobley. PhD, UC Davis 2004. BS, UC Davis 2000. Phone: 949.385.2436. Office: 3134B Nat. Sci. I. Sensitivity in binding free energies due to protein reorganization", in J. Chem. Theory. Comput. Calculating Partition Coefficients of Small Molecules in Octanol/Water and Cyclohexane/Water", in J. Chem. Theory. Comput. See more publications ». One major emphasis is binding prediction. Free energy techniques for predicting binding affinities using molecular simulations. (See alchemistry.org. Version of...

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alchemistry.org

AlchemistryWiki

Alchemical free energy calculations employ unphysical ("alchemical") intermediates to estimate the free energies of various physical processes. Such process include ligand binding to a protein receptor, the transfer of a small molecule from gas to water, or the free energy of a mutation of a side chain. This approach provides not only a quantitative and rigorous method for computing free energies, but often provides insight into the dominant interactions driving binding. With over 700 articles. And p...

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